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[Taxacom] Minimum standards for e-voucher documentation (was Provisions to the Code)

John Grehan calabar.john at gmail.com
Mon Apr 21 14:28:28 CDT 2014 

To be clear, it was not the collection manager who allowed this to happen.
I would hope that any barcoding team would not let themselves be in a
position to be working on collections without direct and immediate
supervision as this particular team apparently did.

In this case the process did not begin with a mess, but apparently created
one.

The under resourcing is not at issue - should have been excluded from the
original posting.

John Grehan


On Mon, Apr 21, 2014 at 2:28 PM, Alex Borisenko <aborisen at uoguelph.ca>wrote:

> IF the following description is correct, then lack of proper curatorial
> oversight of the collection in question is an even bigger problem. What
> kind of a collections manager would let in a bunch of students do
> free-for-all destructive sampling in their collection without supervision?
> Also, what is the issue with barcoding
> unidentified/misidentified/tentatively identified specimens or those from
> undescribed species? Barcoding is a tool designed to help with taxonomic
> validation, so it is to be expected that the construction of reference
> libraries is an iterative process that often begins with a mess. Finally,
> please name one large collection that is not under-resourced...
> AB
>
> ------------------------------
> *From: *"John Grehan" <calabar.john at gmail.com>
> *To: *"Alex Borisenko" <aborisen at uoguelph.ca>
> *Cc: *"David Campbell" <pleuronaia at gmail.com>, "taxacom" <
> taxacom at mailman.nhm.ku.edu>
> *Sent: *Monday, April 21, 2014 2:05:05 PM
>
> *Subject: *Re: [Taxacom] Minimum standards for e-voucher documentation
> (was Provisions to the Code)
>
> If the following description is correct then the lack of quality control
> would seem to be a really major problem:
>
>
>
> ?A team from [country omitted] moved in and badly damaged the collection
> in a massive knock legs off everything project. They confused species put
> material back in the wrong place and damaged hundreds of specimens. They
> did not talk to us at all. They bar-coded undescribed species or unplaced
> specimens or species without a clue as to why they were where they were in
> the collection. Students did the work so they massively miss interpreted
> the collection and of course took absolutely no account of the varying
> degrees of reliability of identifications existing in any large
> under-resourced collection.
>
>
> On Mon, Apr 21, 2014 at 12:25 PM, Alex Borisenko <aborisen at uoguelph.ca>wrote:
>
>> Hi David,
>>
>> Your critical comment below relates to two separate issues:
>> 1. The lack of convenient feedback tools for reporting identification
>> errors in online data portals for DNA barcoding information;
>> 2. The poor quality of data submitted to such portals.
>>
>> With regards to #2, I can only say that the data are as good as we
>> (collectively) make them. E.g., many providers of specimen provenance
>> information do not indicate (and often do not know) the name of the
>> identifier at the time of submission.
>>
>> With regards to #1, I must note that such tools are available. For
>> example, the Barcode of Life Data System has an attribution section for
>> each specimen record that denotes the name of the identifier (when
>> available) and the name of the project manager who could be asked to
>> address taxonomic problems within a particular dataset. E.g., see public
>> BOLD record below (bottom right corner):
>>
>> http://v3.boldsystems.org/index.php/Public_RecordView?processid«SMS268-06
>>
>> Because of privacy/spam concerns, it is not possible to email the
>> identifier or project manager directly from a public specimen record - this
>> functionality is only open to registered BOLD users who are logged in.
>> However, if users wish to provide instant feedback, they have the option
>> to annotate the data record by clicking the Add Tags&Comments button just
>> above the taxonomy - this will flag the record for future users.
>> They can also add tags on the corresponding BIN page which would annotate
>> all specimens putatively referred to a given species:
>>
>> http://v3.boldsystems.org/index.php/Public_BarcodeCluster?clusteruri=BOLD:ACF2193
>>
>> I am not sure if I fully understand your remarks about 'proper' or
>> 'correct' identifiers. If you imply that some barcode data records are
>> contributed by people without adequate taxonomic expertise or
>> accreditation, I personally think that it is a strength of such large-scale
>> data projects.
>> In most other real world situations, the 'proper' and 'correct'
>> identifiers are those who get acknowledged in specialized taxonomic
>> revisions, whereas many of the the 'incorrect' and 'improper' ones write
>> volumes of ecological assessment and biodiversity survey reports whose
>> baseline data never get digitally annotated, let alone cross-referenced
>> against museum collections or taxonomy databases. Ironically, such reports
>> probably have more weight in environmental decision-making. I think that
>> having information from different sources in one digital system where
>> taxonomic inconsistencies become glaringly visible is a step in the right
>> direction. Thank you for your efforts in trying to clean up the resulting
>> taxonomic issues.
>>
>> Best wishes
>> Alex
>>
>>
>>
>> ----- Original Message -----
>>
>> From: "David Campbell" <pleuronaia at gmail.com>
>> Cc: taxacom at mailman.nhm.ku.edu
>> Sent: Monday, April 21, 2014 10:29:38 AM
>> Subject: Re: [Taxacom] Minimum standards for e-voucher documentation (was
>> Provisions to the Code)
>>
>> Quality information is critical, but it's difficult to formulate a
>> standard
>> when different taxa vary greatly in their key features. For many animals,
>> dissection showing reproductive features is critical, and often
>> challenging
>> *(e.g*., microscopic). Others have key differences in a specific part.
>> Barcodes have great potential for facilitating identification, but only if
>> the validity of the barcode is tested for the group in question and
>> specimens are carefully identified.
>> As with any online compilation, content must be accompanied by appropriate
>> curation. There needs to be a quick way to communicate information (such
>> as corrected identification) to a responsible party. In the case of
>> barcoding, where often large numbers of specimens are quickly processed,
>> it's particularly important to have a clearly designated identifier for a
>> particular specimen. It's frustrating to notice an error in a barcoding
>> project, search through several pages to finally find some contact
>> information, and then be told that the submitted identifier (the one used
>> in GenBank) was not the proper identifier to enable them to tell which
>> specimen had the problem. At least they could have given some sort of clue
>> as to what the correct identifier would have been ("the one where you've
>> got a photo of something from a different order" wouldn't do, either).
>>
>>
>> On Mon, Apr 21, 2014 at 2:15 AM, Schindel, David <schindeld at si.edu>
>> wrote:
>>
>> > The Consortium for the Barcode of Life (CBOL) is leading the Barcode of
>> > Wildlife Project on endangered species. We will be grappling with the
>> > issue of what minimum documentation should be required for occurrence
>> > records and BARCODE records in GenBank when there is no traditional
>> voucher
>> > specimen (e.g., dead animal bones and skin or a herbarium sheet). This
>> has
>> > special significance in the project which is constructing a reference
>> > library of barcode records in GenBank that will be used to identify the
>> > species of organisms involved in the investigation and prosecution of
>> > wildlife crime. We're all familiar with circumstances in which a
>> > traditional voucher specimen is either impractical (e.g., endangered
>> whales
>> > or other large species) or illegal (endangered/protected species). There
>> > was a small literature on 'e-vouchers' a few years ago but as far as I
>> > know, it never evolved to the level of a proposed standard for
>> > documentation.
>> >
>> > This is related to the ongoing thread about holotypes but I stress that
>> we
>> > are not trying to erect new species without a traditional type specimen.
>> > Rather, we want to provide a credible way for someone to verify the
>> > species identification of a specimen with a GenBank record when there
>> is no
>> > traditional voucher. Tissue samples, photographs, geolocation,
>> > measurements and environmental context data are the obvious elements in
>> > such a standard. Do any of you know of an effort to formalize these
>> > minimum information standards?
>> >
>> > Thanks and regards,
>> >
>> > David Schindel
>> >
>> > -----Original Message-----
>> > From: taxacom-bounces at mailman.nhm.ku.edu [mailto:
>> > taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of laurent raty
>> > Sent: Wednesday, April 16, 2014 6:23 AM
>> > To: taxacom at mailman.nhm.ku.edu
>> > Subject: Re: [Taxacom] [iczn-list] provisions to the Code
>> >
>> > - "Physical specimen" is not a term regulated by the ICZN. In fact, the
>> > word "physical" appears exactly zero times in the entire text of the
>> > Code; and given the definition of "specimen" there, an "un-physical
>> > specimen" (Stephen used the word "ghost" recently) seems to be an
>> > impossibility. Specimens are always physical, or they would be no
>> > specimens.
>> >
>> > - What comes closest in the ICZN to what some seem to call "physical
>> > specimen" is "extant specimen" ("sp?cimens qui existent toujours" in the
>> > French text).
>> >
>> > - For names published after 1999, Art.16.4.2 gives explicit additional
>> > requirements for availability in the special case where the holotype or
>> > syntypes are extant specimens. As this is clearly treated as a special
>> > case, it is obvious that having extant specimens as types cannot be
>> > understood as a general requirement for all species-group names
>> > published after 1999.
>> >
>> > - Again, it is a complete misreading to pretend that:
>> > "73.1.4. Designation of an illustration of a single specimen as a
>> > holotype is to be treated as designation of the specimen illustrated;
>> > the fact that the specimen no longer exists or cannot be traced does not
>> > of itself invalidate the designation."
>> > ...introduces an exception to a general "rule" that would say that a
>> > holotype must be an extant specimen. Should such a "rule" exist, this
>> > article would actually not allow any exception to it: the designation of
>> > the illustrated specimen would be allowed only if the specimen is
>> > extant; the designation of the illustration would have to be treated as
>> > the designation of the specimen; thus, should the specimen not be
>> > extant, the designation of the illustration would not be allowed.
>> >
>> > The truth is that there is NO such rule in the Code.
>> >
>> > My two cents,
>> > Laurent -
>> >
>> >
>> >
>> >
>> >
>> >
>> > On 04/16/2014 09:48 AM, Paul van Rijckevorsel wrote:
>> > > From: "Weakley, Alan" <weakley at bio.unc.edu>
>> > > Sent: Wednesday, April 16, 2014 1:38 AM
>> > >
>> > >> Hi all: here is the current code for algae, fungi, and plants
>> > >> (
>> >
>> https://urldefense.proofpoint.com/v1/url?u=http://www.iapt-taxon.org/nomen/main.php?page%3Dtitle&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r”xk%2BkvyzF5zfdS9tDhVEg%3D%3D%0A&m=BWWddgspb8VyrOJmwD7URzKSH%2BOlLYhcK7fpJhBFDHo%3D%0A&sá234d69e54d95922d340300d45e3d1719a2e98c46bb13d43b448028992f9e95
>> > )
>> > >
>> > >> Bottom line: after 2007, physical specimen only (exceptions as noted
>> > >> below).
>> > >
>> > > ***
>> > > This is not particularly accurate. Illustrations may be
>> > > types, and the date of 1 January 2007 does not change
>> > > that; such illustrations as were types before that date will
>> > > continue to be so after that date. And new designations
>> > > of illustrations as types may still be made after that date.
>> > >
>> > > What has changed with 1 January is that names of new
>> > > species or new infraspecific taxa may not have an
>> > > illustration as a type (exceptions excepted).
>> > >
>> > > Paul
>> > >
>> > >
>> > > _______________________________________________
>> > > Taxacom Mailing List
>> > > Taxacom at mailman.nhm.ku.edu
>> > >
>> >
>> https://urldefense.proofpoint.com/v1/url?u=http://mailman.nhm.ku.edu/mailman/listinfo/taxacom&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r”xk%2BkvyzF5zfdS9tDhVEg%3D%3D%0A&m=BWWddgspb8VyrOJmwD7URzKSH%2BOlLYhcK7fpJhBFDHo%3D%0A&sÙf54cf48371af1f22f8c4749482432199c25b34415db3e7d8dba08f199e5f01
>> > > The Taxacom Archive back to 1992 may be searched at:
>> >
>> https://urldefense.proofpoint.com/v1/url?u=http://taxacom.markmail.org/&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r”xk%2BkvyzF5zfdS9tDhVEg%3D%3D%0A&m=BWWddgspb8VyrOJmwD7URzKSH%2BOlLYhcK7fpJhBFDHo%3D%0A&sZ6347632a4f57b5937d5523780efebac85be4516d4c8a98ff9ca27b191e26b2
>> > >
>> > > Celebrating 27 years of Taxacom in 2014.
>> > >
>> >
>> > _______________________________________________
>> > Taxacom Mailing List
>> > Taxacom at mailman.nhm.ku.edu
>> >
>> >
>> https://urldefense.proofpoint.com/v1/url?u=http://mailman.nhm.ku.edu/mailman/listinfo/taxacom&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r”xk%2BkvyzF5zfdS9tDhVEg%3D%3D%0A&m=BWWddgspb8VyrOJmwD7URzKSH%2BOlLYhcK7fpJhBFDHo%3D%0A&sÙf54cf48371af1f22f8c4749482432199c25b34415db3e7d8dba08f199e5f01
>> > The Taxacom Archive back to 1992 may be searched at:
>> >
>> https://urldefense.proofpoint.com/v1/url?u=http://taxacom.markmail.org/&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r”xk%2BkvyzF5zfdS9tDhVEg%3D%3D%0A&m=BWWddgspb8VyrOJmwD7URzKSH%2BOlLYhcK7fpJhBFDHo%3D%0A&sZ6347632a4f57b5937d5523780efebac85be4516d4c8a98ff9ca27b191e26b2
>> >
>> > Celebrating 27 years of Taxacom in 2014.
>> >
>> > _______________________________________________
>> > Taxacom Mailing List
>> > Taxacom at mailman.nhm.ku.edu
>> > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> > The Taxacom Archive back to 1992 may be searched at:
>> > http://taxacom.markmail.org
>> >
>> > Celebrating 27 years of Taxacom in 2014.
>> >
>>
>>
>>
>> --
>> Dr. David Campbell
>> Assistant Professor, Geology
>> Department of Natural Sciences
>> Box 7270
>> Gardner-Webb University
>> Boiling Springs NC 28017
>> _______________________________________________
>> Taxacom Mailing List
>> Taxacom at mailman.nhm.ku.edu
>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> The Taxacom Archive back to 1992 may be searched at:
>> http://taxacom.markmail.org
>>
>> Celebrating 27 years of Taxacom in 2014.
>>
>> _______________________________________________
>> Taxacom Mailing List
>> Taxacom at mailman.nhm.ku.edu
>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> The Taxacom Archive back to 1992 may be searched at:
>> http://taxacom.markmail.org
>>
>> Celebrating 27 years of Taxacom in 2014.
>>
>
>
>

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